clovr: a virtual machine for automated and portable...
TRANSCRIPT
CloVR: A virtual machine for automated and portable sequence
analysis from the desktop using cloud computing
Mikk Eelmets Journal Club 10.10.2011
http://pathogenomics.bham.ac.uk/hts/
http://genome.wellcome.ac.uk/doc_WTX059576.html
Tools for microbial genomics
• Workflow systems and workbenches: Galaxy, Ergatis, GenePattern, Taverna …
• Bioinformatics services: RAST, MG-RAST, ISGA, IGS Annotation engine …
• Portable software packages: Mothur, Qiime, DIYA …
• New tool: Cloud Virtual Resource (CloVR)
Architecture of the CloVR application
Pipelines provided in the CloVR
CloVR analysis protocols
Components of the CloVR VM
Steps of an automated pipeline in CloVR
Data transfer between instances
Performance
250,000 454 FLX Titanium 8 kb paired-end sequencing reads of the bacterium Acinetobacter baylyi totaling ~89 Mbp and expected to cover the ~3.5 Mbp genome at 25-fold coverage
Execution profile
500,000 3 kbp paired-end sequence reads generated with the 454 Titanium FLX platform from a Escherichia coli whole-genome shotgun library
Conclusion • CloVR is portable virtual machine that
provides automated analysis pipelines for microbial genomics
• Sophisticated analysis can be done using cloud computing platforms (Amazon EC2 Cloud, Nimbus Science Clouds etc)
• User-friendly interface for scientists without a bioinformatics background
• Can be modified or adapt for specific goals
Reference Angiuoli SV, Matalka M, Gussman A, Galens K, Vangala M, Riley DR,
Arze C, White JR, White O, Fricke WF.
" CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. “
BMC Bioinformatics. 2011 Aug 30;12:356.
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